TEGUCIGALPA, HONDURAS — The number of murders the Honduran drug lord admitted to orchestrating over 10 years was stunning.

The dead included people he described as killers, rapists and gang members. Then there were the innocents: a lawyer, two journalists, a Honduran refugee in Canada, an official who was serving as Honduras’s antidrug czar and a politician who became his adviser; there were even two children caught in a shootout.

In all, the drug lord, Devis Leonel Rivera Maradiaga, said that, working in concert with drug traffickers and others, he had “caused” the deaths of 78 people — a number that posed a dilemma for United States officials when Mr. Rivera came to them offering to expose high-level corruption in this Central American nation of some nine million people.

Knowing that he was already in the sights of United States investigators, Mr. Rivera sought to help the Drug Enforcement Administration root out corrupt Honduran politicians and other elites who had made Honduras a gateway for massive amounts of cocaine headed for the United States through Mexico.

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Devis Leonel Rivera Maradiaga, left, and Javier Eriberto Rivera Maradiaga. The brothers led a drug trafficking organization called Los Cachiros that was said to be responsible for dozens of murders.CreditDepartment of the Treasury Office of Foreign Assets Control

The offer came at a time when United States officials were deeply concerned by Honduras’s slide into anarchy. A stalwart ally and home to a United States military base, Honduras was plagued by drug traffickers and gangs and had one of the world’s highest homicide rates. It is the first landing point for about 80 percent of suspected drug flights departing from South America, the State Department has said.

But to sign Mr. Rivera to a formal cooperation agreement meant the government would most likely have to do something for him: seek leniency on his behalf, which could spare him a long prison sentence and leave the families of the Honduran victims believing that Mr. Rivera got away with murder.

Today, four years after Mr. Rivera’s clandestine cooperation began, federal prosecutors in Manhattan have with his help charged seven police officers from Honduras’s national force, along with the son of the country’s former president and several members of a prominent Honduran banking family.

The evidence, a prosecutor said at a hearing on Sept. 5, showed nothing short of “state-sponsored drug trafficking.”

Investigators have also gathered evidence that Honduras’s former president, Porfirio Lobo, took bribes to protect traffickers, and that drug money may have helped finance the rise of the country’s current president, Juan Orlando Hernández.

Neither politician has been charged and, through representatives, both vigorously denied the allegations to The New York Times.

Here in the capital city, which sits in a bowl ringed by mountains, there has been much speculation about who will next face charges in New York, some of it fueled by the American embassy, which took the unusual step of posting a list of Hondurans, including current military officers, under investigation for drug trafficking and corruption.

Prosecutors have long enlisted cooperators with violent backgrounds to achieve the greater goal of taking down a Mafia leader or some violent gang. Salvatore Gravano, the former underboss of the Gambino crime family in New York who became a government informer, admitted to killing 19 people.

In the Honduras case, prosecutors who approved the agreement with Mr. Rivera and a second deal with his brother, Javier, say the men offered a rare opportunity to expose the links between drug traffickers and Honduran politicians and businessmen.

“The illegal drug trade in Honduras not only infected much of its civil society, including the highest levels of government and its financial sector, but also brought frightening levels of violence on its people,” Joon H. Kim, the acting United States attorney in Manhattan, said in a statement.

Details of Devis Rivera’s cooperation, which included surreptitiously recording Honduran targets, emerged in March when he testified over two days against Fabio Lobo, the former Honduran president’s son. Mr. Lobo was recently sentenced to 24 years in prison for cocaine conspiracy.

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A police officer approaching a home in the La Era neighborhood of Tegucigalpa. Many officers have been dismissed on charges of corruption tied to the drug trade.CreditDaniele Volpe for The New York Times

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A suspect arrested in the San Miguel neighborhood of Tegucigalpa, with packets of what was suspected to be cocaine on the desk next to him.CreditDaniele Volpe for The New York Times

Murdering a General

The Rivera brothers, who led a trafficking organization called Los Cachiros, built a fortune as middlemen, moving cocaine from hidden airstrips northward to the Mexican cartels.

The brothers used violence to muscle out rivals and others, from at least 2003 when Devis Rivera was involved in the murder of a hospital security guard and, the next year, the killing of the man he had been guarding, a Honduran cartel leader.

By late 2009, Mr. Rivera testified that he and other traffickers felt threatened by Gen. Julián Arístides González Irías, the Honduran counternarcotics czar. The American embassy in Tegucigalpa once described General Arístides González as the “last (somewhat) best hope” to revive Honduras’s counternarcotics efforts, according to a cable published by WikiLeaks.

Mr. Rivera testified that the traffickers paid $200,000 to $300,000 for the killing, which was handled by a group of police officers.

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Cadets from the General Francisco Morazan Military Academy stood guard at the 2009 funeral of General Julián Arístides González Irías, a counternarcotics czar who was killed by a gunman on a motorcycle.CreditOrlando Sierra/Agence France-Presse — Getty Images

That was around the same time, Mr. Rivera testified, that he and his brother bought a president.

Concerned about the possibility of extradition to the United States, Mr. Rivera said they paid more than $400,000 in bribes to President Porfirio Lobo, before and after his November 2009 election. At President Lobo’s home in early 2010, Mr. Rivera received the assurance he wanted.

“The president said to me to tell my brother not to worry,” Mr. Rivera recalled, “because during his four-year term nobody would get extradited.”

President Lobo also designated his son Fabio, who was once a juvenile court judge, “as a middleman who would be able to protect us, help us — the Cachiros,” Mr. Rivera said.

Fabio Lobo became a valuable ally. “I gave him a bribe almost every time I met with him,” Mr. Rivera said. “I knew that having him with me, everything would go well.”

One time, the president’s son, riding with his armed security detail in a convoy of blue Prado SUVs, escorted 1,000 kilograms of cocaine for the brothers through a police checkpoint.

He “lowered the windows a little bit and then started talking with the police officers,” Mr. Rivera recalled.

By Mr. Rivera’s account, the president’s son threw himself into his new role, asking to visit a backcountry airstrip to “feel the adrenaline — what you experience when you receive a plane loaded with drugs.”

“I’d do anything for you,” Fabio Lobo said in one recorded conversation. “I’ll go to the moon and back for you.”

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The former president of Honduras, Porfirio Lobo Sosa, in 2012. The authorities are investigating allegations that he took bribes to protect drug traffickers.CreditAlexandre Meneghini/Associated Press

With President Lobo’s patronage, the brothers invested in construction companies that competed for government contracts. In the fashion of Pablo Escobar, they opened a zoo, complete with tigers, jaguars, and lions. The brothers also developed relationships with one of the country’s most prominent families, the Rosenthals, who acted as their bankers and money launderers. They invested drug proceeds in cattle, with their beef later exported to the United States, and agriculture.

Brian H. Bieber, a lawyer for former President Lobo, said his client remains under investigation by the American authorities. He said that the situation has been frustrating for Mr. Lobo, who has been “loud and clear in his emphatic denial” of Mr. Rivera’s allegations.

“There is absolutely no credible evidence to support the allegations made by an admitted mass murderer and a convicted drug trafficker,” Mr. Bieber said, adding that the former president had “absolutely no” relationship with the Cachiros.

As President Lobo’s term neared its end in 2013, Mr. Rivera had new concerns.

The United States Treasury Department had announced sanctions against the Rivera brothers, and Honduran authorities began seizing their assets, worth hundreds of millions of dollars, even their zoo.

“I was afraid for my life. I was afraid for my family,” Mr. Rivera testified. “I could get killed because I had worked with politicians, police officers.”

By December 2013, Mr. Rivera testified, he and his brother Javier had begun talking with the D.E.A. and prosecutors to try to strike a deal.

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A zoo that the Rivera brothers opened in Santa Cruz de Yojoa was seized by the government.CreditDaniele Volpe for The New York Times

A Devil’s Bargain

Prosecutors wrestled with the idea of granting a deal to men who had killed so many people, particularly innocents, according to current and former government officials.

Little has been said about how that deal began. On Dec. 5, 2013, Mr. Rivera and his lawyer met with the D.E.A. and at least one prosecutor at a secret session in Belize, according to one document. In all, about 20 sessions were held, the document shows.

“We were trying to corroborate what they were telling us, obviously, through that process,” a senior D.E.A. official said.

One official said prosecutors were not aware of how many murders Mr. Rivera had been involved in — only his role in drug trafficking — until after the discussions began.

Under a cooperation deal, the brothers would have to admit to — and plead guilty to — all murders and other crimes they had ever committed, even those the authorities were unaware of. That would sweep in killings that might otherwise go unaccounted for in Honduras.

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The body of the television anchor Anibal Barrow being removed from a field in the outskirts of San Pedro Sula on July 9, 2013. The authorities said Mr. Barrow was kidnapped and killed under the direction of the Rivera brothers.CreditAssociated Press

“A guilty plea as part of cooperation is often the only way the defendant can be held accountable,” Mr. Kim, the acting United States attorney, said, speaking generally.

Mr. Rivera’s agreement shows that if he fulfilled his end of the deal, prosecutors would seek leniency at his sentencing. He may also be placed in the witness protection program, the document says. Some of his relatives have already been permitted to move to the United States, Mr. Rivera testified.

The extent of the Rivera brothers’ assistance continues to become public in court proceedings. This summer, the government filed a D.E.A. search warrant application showing that in 2013, Mr. Rivera secretly recorded a conversation with another Honduran trafficker who claimed to have made a $250,000 payment intended for Juan Orlando Hernández, who later became Honduras’s president. The document does not indicate that Mr. Hernández ever received the money.

Mr. Hernández’ office responded that it was unaware, until an inquiry by The Times, of this allegation in the D.E.A. document. It attributed the claim to drug traffickers who have been targeted by Mr. Hernández’s own government’s anti-narcotics campaign.

“It is logical and even predictable that criminals who have been damaged by the actions of our government feel hatred and resentment against those who have made those decisions,” Mr. Hernández’s office wrote in a statement.

The president’s office said that the administration’s fight against drug traffickers has resulted in 14 extraditions and the destruction of 150 clandestine landing strips.

During President Hernández’s tenure, Honduras’s murder rate has fallen. About a third of the police force has been dismissed following revelations of some officers’ roles in drug-related assassinations.

Still, a recent State Department report observed that in Honduras, “new criminal bosses have emerged to assume leadership of dismantled networks to continue cocaine smuggling and other forms of crime.”

Mr. Rivera has indicated he has lived up to his end of the bargain.

“What I did was confess all the crimes that I have committed,” he testified. “The work I have done with them has been to give them information, all the information I knew, about my work with drug trafficking and politicians.”

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Shooting practice at the Police Technological Institute.CreditDaniele Volpe for The New York Times

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A class at the institute.CreditDaniele Volpe for The New York Times

Contaminated Justice

In Honduras, there is relief Mr. Rivera is facing justice in New York.

“They should be judged here, but by whom?” said Hilda Caldera, the widow of Alfredo Landaverde, a politician and counternarcotics official who was assassinated in December 2011 — one of the murders to which Mr. Rivera has pleaded guilty. “The justice here is contaminated.”

In an interview at the national university where she teaches, Ms. Caldera said her husband had been willing to declare what few others would say publicly: that traffickers had infiltrated the police and military.

“He was alone, so alone, in talking about this,” she said.

Mr. Landaverde’s name appears on a spreadsheet, titled Appendix A, that is part of Mr. Rivera’s plea agreement. The three-page document lists the 78 murders through 2013 that Mr. Rivera admitted involvement in.

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Police officers and hospital workers in 2011 around the body of Mr. Landaverde, the former government adviser. Devis Leonel Rivera Maradiaga has pleaded guilty to his murder.CreditFernando Antonio/Associated Press

The names of 49 victims are listed only partially or as “FNU LNU” — first and last names unknown — and other details where available.

One was “an assassin believed to have worked for the Echeverria-Ramos family.” Several were “suspected” murderers and rapists.

Twenty-nine victims are named in full, including Mr. Landaverde, the 51st entry.

One victim’s father, Heriberto Palacios, said he long doubted that whoever ordered the killing of his son, Nahum, would be held to account, and he was uneasy at the prospect of leniency for the Rivera brothers, given “all of the evil they did in Honduras.”

His son had been a prominent television and radio reporter, an advocate for farmers locked in a bloody struggle with large landowners. In 2010, Nahum and his girlfriend, Yorleny Sánchez, a doctor, were fatally shot near his home. They are victims Nos. 23 and 24.

Mr. Palacios, a retired farm laborer, said he had once gone to a local government office to inquire about his son’s murder investigation. He said officials refused to provide any information, lest he “might misinterpret it.”

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Mr. Landaverde’s widow recalled her husband’s outspokenness about drug traffickers infiltrating the police and military. “He was alone, so alone, in talking about this,” she said.CreditDaniele Volpe for The New York Times

A version of this article appears in print on , on Page A1 of the New York edition with the headline: Murderous Drug Lord Helps U.S. in Secret Deal. Order Reprints | Today’s Paper | Subscribe